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1
المؤلفون: Michael C. Thompson, Thomas A. Bobik, Christopher S. Crowley, Todd O. Yeates, Jeffery S. Kopstein
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1584-1590
مصطلحات موضوعية: Protein Conformation, Biophysics, Shell (structure), Crystallography, X-Ray, Biochemistry, Cobalamin, Cofactor, chemistry.chemical_compound, Protein structure, Bacterial Proteins, Structural Biology, Bacterial microcompartment, polycyclic compounds, Genetics, Structural Communications, Cloning, Molecular, biology, nutritional and metabolic diseases, Condensed Matter Physics, Transport protein, Vitamin B 12, chemistry, Cytoplasm, biology.protein, Function (biology)
الوصف: The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein–ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.
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2
المؤلفون: George Kontopidis, Anna Nordle Gilliver, Lindsay Sawyer
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1498-1503
مصطلحات موضوعية: Sheep, Milk protein, Biophysics, food and beverages, High resolution, Lactoglobulins, Crystal structure, Biology, Triclinic crystal system, Crystallography, X-Ray, Milk Proteins, Condensed Matter Physics, Biochemistry, Protein Structure, Secondary, respiratory tract diseases, Protein Structure, Tertiary, Transport protein, Crystallography, Structural Biology, Atomic resolution, Genetics, Structural Communications, Animals, Cattle
الوصف: The crystal structure of the triclinic form of the milk protein β-lactoglobulin from sheep (Ovis aries) at 1.1 Å resolution is described together with a comparison of the triclinic structures of the low-pH bovine and high-pH ovine proteins. All three structures are remarkably similar, despite the well known pH-dependent conformational transition described for the bovine and porcine proteins that occurs in solution. The high resolution of the present structure determination has allowed a more accurate description of the protein than has hitherto been possible, but it is still not clear whether flexibility changes in the external loops can compensate for the presence of a significant void in the unliganded interior of the structure.
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3
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1485-1491
مصطلحات موضوعية: medicine.drug_class, Stereochemistry, Molecular Sequence Data, Antibiotics, Biophysics, Phenylalanine, Crystal structure, Biology, Crystallography, X-Ray, medicine.disease_cause, Biochemistry, Protein Structure, Secondary, Bacterial Proteins, Structural Biology, Genetics, medicine, Structural Communications, Shikimate pathway, Amino Acid Sequence, Tyrosine, Hydro-Lyases, chemistry.chemical_classification, Pseudomonas aeruginosa, Tryptophan, Condensed Matter Physics, Enzyme, chemistry
الوصف: Pseudomonas aeruginosacauses opportunistic infections and is resistant to most antibiotics. Ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital forP. aeruginosabut are absent in mammals. One such enzyme, type II dehydroquinase (DHQase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. This step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aromatic metabolites. The recombinant expression, purification and crystal structure of catalytically active DHQase fromP. aeruginosa(PaDHQase) are presented. Cubic crystals belonging to space groupF23, with unit-cell parametersa=b=c= 125.39 Å, were obtained by vapor diffusion in sitting drops and the structure was refined to anRfactor of 16% at 1.74 Å resolution. PaDHQase is a prototypical type II DHQase with the classical flavodoxin-like α/β topology.
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4
المؤلفون: Thomas A. Bobik, Mark A. Arbing, Madeline E. Rasche, Michael R. Sawaya, Erick J. Morales, Todd O. Yeates, Duilio Cascio, Annie Shin
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1472-1479
مصطلحات موضوعية: Biophysics, Methanofuran, Biochemistry, Protein Structure, Secondary, Cofactor, chemistry.chemical_compound, Bacterial Proteins, Biosynthesis, Structural Biology, Genetics, Structural Communications, Furans, chemistry.chemical_classification, Binding Sites, Crystallography, biology, Tetrahydromethanopterin, Active site, Methanocaldococcus jannaschii, Condensed Matter Physics, biology.organism_classification, Recombinant Proteins, Protein Structure, Tertiary, Pterins, Amino acid, chemistry, Methanocaldococcus, biology.protein, Archaea
الوصف: Prior studies have indicated that MJ1099 fromMethanocaldococcus jannaschiihas roles in the biosynthesis of tetrahydromethanopterin and methanofuran, two key cofactors of one-carbon (C1) metabolism in diverse organisms including the methanogenic archaea. Here, the structure of MJ1099 has been solved to 1.7 Å resolution using anomalous scattering methods. The results indicate that MJ1099 is a member of the TIM-barrel superfamily and that it is a homohexamer. Bioinformatic analyses identified a potential active site that is highly conserved among MJ1099 homologs and the key amino acids involved were identified. The results presented here should guide further studies of MJ1099 including mechanistic studies and possibly the development of inhibitors that target the methanogenic archaea in the digestive tracts of humans and that are a source of the greenhouse gas methane.
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المؤلفون: Ronald E. Stenkamp, Kirk L. Pappan, John C. Reese, David C. Teller, Zicheng Shen, Craig A. Behnke, Gerald R. Reeck
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1480-1484
مصطلحات موضوعية: food.ingredient, Pectin, Biophysics, Dickeya, Biology, medicine.disease_cause, Biochemistry, Protein Structure, Secondary, Cell wall, food, Rice weevil, X-Ray Diffraction, Structural Biology, Botany, Hydrolase, Genetics, medicine, Structural Communications, Animals, Escherichia coli, chemistry.chemical_classification, Sitophilus, food and beverages, Oryza, Condensed Matter Physics, biology.organism_classification, Enzyme, chemistry, Weevils, Carboxylic Ester Hydrolases
الوصف: Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that have been deposited in the last 15 years. Comparison of the structure of the rice weevil pectin methylesterase with that fromDickeya dandantii(formerlyErwinia chrysanthemi) indicates that the reaction mechanisms are the same for the insect, plant and bacterial pectin methylesterases. The similarity of the structure of the rice weevil enzyme to theEscherichia colilipoprotein YbhC suggests that the evolutionary origin of the rice weevil enzyme was a bacterial lipoprotein, the gene for which was transferred to a primitive ancestor of modern weevils and other Curculionidae. Structural comparison of the rice weevil pectin methylesterase with plant and bacterial enzymes demonstrates that the rice weevil protein is circularly permuted relative to the plant and bacterial molecules.
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6Structure of anAspergillus fumigatusold yellow enzyme (EasA) involved in ergot alkaloid biosynthesis
المؤلفون: Ashley L. Ellis, Audrey L. Lamb, Annemarie S. Chilton
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1328-1332
مصطلحات موضوعية: Models, Molecular, Ergot Alkaloids, Flavin Mononucleotide, Stereochemistry, Old yellow enzyme, Biophysics, Crystallography, X-Ray, Biochemistry, Aldehyde, Protein Structure, Secondary, Aspergillus fumigatus, Fungal Proteins, chemistry.chemical_compound, Structural Biology, Oxidoreductase, Catalytic Domain, Genetics, Structural Communications, chemistry.chemical_classification, biology, ATP synthase, NADPH Dehydrogenase, Active site, Condensed Matter Physics, biology.organism_classification, Amino acid, Monomer, chemistry, biology.protein
الوصف: TheAspergillus fumigatusold yellow enzyme (OYE) EasA reduces chanoclavine-I aldehyde to dihydrochanoclavine aldehyde and works in conjunction with festuclavine synthase at the branchpoint for ergot alkaloid pathways. The crystal structure of the FMN-loaded EasA was determined to 1.8 Å resolution. The active-site amino acids of OYE are conserved, supporting a similar mechanism for reduction of the α/β-unsaturated aldehyde. The C-terminal tail of one monomer packs into the active site of a monomer in the next asymmetric unit, which is most likely to be a crystallization artifact and not a mechanism of self-regulation.
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المؤلفون: Norbert Schormann, Surajit Banerjee, Debasish Chattopadhyay, Chapelle A. Ayres, Alexandra Fry, Glen C. Ulett, Olga Senkovich
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1333-1339
مصطلحات موضوعية: Models, Molecular, Surface Properties, Molecular Sequence Data, Biophysics, Dehydrogenase, Crystallography, X-Ray, medicine.disease_cause, Biochemistry, Cofactor, Streptococcus agalactiae, Conserved sequence, Bacterial Proteins, stomatognathic system, Structural Biology, Oxidoreductase, Catalytic Domain, Genetics, medicine, Structural Communications, Amino Acid Sequence, Protein Structure, Quaternary, Peptide sequence, Conserved Sequence, Glyceraldehyde 3-phosphate dehydrogenase, chemistry.chemical_classification, biology, Glyceraldehyde-3-Phosphate Dehydrogenases, NAD, Condensed Matter Physics, Molecular biology, chemistry, Structural Homology, Protein, biology.protein, NAD+ kinase, Protein Binding
الوصف: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH fromStreptococcus agalactiaein complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294–307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.
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8
المصدر: Acta Crystallographica. Section F, Structural Biology Communications
مصطلحات موضوعية: Acinetobacter baumannii, Models, Molecular, Rossmann fold, Acinetobacter baumannii WM99c, Genomic Islands, Molecular Sequence Data, Biophysics, Dehydrogenase, Reductase, Crystallography, X-Ray, Biochemistry, Apoenzymes, Bacterial Proteins, multidrug resistance, Structural Biology, Catalytic Domain, Genomic island, Genetics, Structural Communications, NADH, NADPH Oxidoreductases, Amino Acid Sequence, Peptide sequence, Short-chain dehydrogenase, biology, opportunistic pathogen, Active site, Condensed Matter Physics, biology.organism_classification, biology.protein, Fatty Acid Synthases, Genome, Bacterial, nosocomial strain
الوصف: The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified.
Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access. -
9
المؤلفون: Idania E. Quintero-Reyes, Vivian Stojanoff, Alonso A. Lopez-Zavala, Jesus S. Carrasco-Miranda, Rogerio R. Sotelo-Mundo, Enrique Rudiño-Piñera, Andrzej Weichsel
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1150-1154
مصطلحات موضوعية: Models, Molecular, Purine, animal structures, Pyrimidine, Protein Conformation, Biophysics, Biology, Crystallography, X-Ray, Biochemistry, chemistry.chemical_compound, Structural Biology, Crustacea, Ribose, Genetics, Animals, Structural Communications, Transferase, Nucleotide, chemistry.chemical_classification, fungi, Isothermal titration calorimetry, Purine Nucleosides, Pyrimidine Nucleosides, Condensed Matter Physics, Nucleoside-diphosphate kinase, chemistry, Nucleoside-Diphosphate Kinase, Crystallization, Nucleoside
الوصف: Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK fromLitopenaeus vannamei(LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry,LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyeset al.(2012),J. Bioenerg. Biomembr.44, 325–331]. In order to investigate the differences in selectivity,LvNDK was crystallized as binary complexes with both acceptor (dADP and dCDP) and donor (ADP) phosphate-group nucleoside diphosphate substrates and their structures were determined. The three structures with purine or pyrimidine nucleotide ligands are all hexameric. Also, the binding of deoxy or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 2′-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide. Because of this, shrimp NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism.
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المؤلفون: Christopher Ceccarelli, Oluwatoyin A. Asojo
المصدر: Acta Crystallographica Section F Structural Biology Communications. 70:1162-1166
مصطلحات موضوعية: Models, Molecular, Necator americanus, Stereochemistry, Biophysics, Biology, Crystallography, X-Ray, Biochemistry, chemistry.chemical_compound, Structural Biology, Catalytic Domain, Genetics, Animals, Structural Communications, Transferase, Molecular replacement, Heme, Glutathione Transferase, Molecular Structure, Protoporphyrin IX, Zinc protoporphyrin, Glutathione, Condensed Matter Physics, biology.organism_classification, Glutathione S-transferase, chemistry, biology.protein
الوصف: GlutathioneS-transferase 1 fromNecator americanus(Na-GST-1) is a vaccine candidate for hookworm infection that has a high affinity for heme and metal porphyrins. As part of attempts to clarify the mechanism of heme detoxification by hookworm GSTs, co-crystallization and soaking studies ofNa-GST-1 with the heme-like molecules protoporphyrin IX disodium salt, hematin and zinc protoporphyrin were undertaken. While these studies did not yield the structure of the complex ofNa-GST-1 with any of these molecules, co-crystallization experiments resulted in the first structures of the complex ofNa-GST-1 with the substrate glutathione. The structures of the complex ofNa-GST-1 with glutathione were solved from pathological crystalline aggregates comprising more than one crystal form. These first structures of the complex ofNa-GST-1 with the substrate glutathione were solved by molecular replacement from data collected with a sealed-tube home source using the previously reported apo structure as the search model.
